Contacts of the helix formed by residues 395 - 406 (chain D) in PDB entry 1JZ3
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with HIS 395 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144D ASP* 5.8 0.4 + - - -
210D ARG* 3.4 35.1 - - + +
211D ASP* 3.8 24.5 + - - -
358D GLU* 2.8 19.8 + - - +
367D MET* 4.1 24.8 + - + -
368D ASP* 5.9 0.6 - - - -
372D MET* 3.4 16.3 - - + +
394D ASN* 1.3 75.1 - - - +
396D PRO* 1.3 83.7 - - + +
397D LEU* 2.9 35.4 + - + +
398D TRP* 2.9 19.1 + - - +
399D TYR* 3.9 1.6 - - - -
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Residues in contact with PRO 396 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D PRO* 5.2 14.1 - - + -
144D ASP* 4.1 32.3 - - + +
210D ARG* 4.9 0.4 - - - -
211D ASP* 5.5 0.9 - - - +
394D ASN 3.3 5.9 - - - +
395D HIS* 1.3 100.6 - - + +
397D LEU* 1.3 62.2 + - - +
398D TRP 3.2 1.2 + - - -
399D TYR* 3.4 21.5 + - + +
400D THR* 3.7 10.3 + - - -
446D ARG* 4.3 18.6 - - - +
450D HIS* 4.7 3.2 + - - +
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Residues in contact with LEU 397 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369D GLU* 3.6 51.6 - - + +
372D MET* 4.0 8.1 - - - -
395D HIS* 2.9 24.4 + - + +
396D PRO* 1.3 79.4 - - - +
398D TRP* 1.3 64.2 + - - +
400D THR* 3.2 22.6 + - + -
401D LEU* 3.1 34.6 + - + +
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Residues in contact with TRP 398 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356D ARG* 3.6 51.1 - - + -
372D MET* 3.7 37.1 - - + -
375D ASP* 4.7 0.2 - - + -
376D ILE* 3.5 35.9 - - + -
379D MET* 4.4 7.9 - - - -
387D VAL* 4.0 25.8 - - + +
389D CYS* 4.1 13.1 - - - -
394D ASN* 3.3 30.4 + - + -
395D HIS 2.9 14.9 + - - +
397D LEU* 1.3 79.7 - - - +
399D TYR* 1.3 60.6 + + + +
401D LEU* 3.3 4.1 + - - +
402D CYS* 2.8 60.3 + - - -
407D LEU* 4.8 0.9 - - + -
409D VAL* 4.8 1.5 - - + +
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Residues in contact with TYR 399 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389D CYS* 4.1 5.3 - - - -
394D ASN* 2.8 44.6 + - + +
395D HIS 3.9 1.6 - - - -
396D PRO* 3.6 13.5 - - + +
397D LEU 3.3 0.2 - - - -
398D TRP* 1.3 76.3 - + - +
400D THR* 1.4 57.0 + - - +
402D CYS* 3.3 2.3 + - - -
403D ASP* 2.7 40.5 + - - +
409D VAL* 4.3 15.9 - - + -
411D ASP* 2.6 38.9 + - - -
446D ARG* 3.2 21.3 + - - -
447D ASP* 3.3 14.9 + - - -
450D HIS* 3.3 33.4 - + + +
452D SER* 3.5 5.4 + - - -
453D VAL* 3.8 20.4 - - + -
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Residues in contact with THR 400 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329D ASP* 4.6 2.7 - - - +
396D PRO 3.7 6.3 + - - -
397D LEU* 3.2 26.8 + - + +
399D TYR* 1.4 79.8 - - - +
401D LEU* 1.3 64.5 + - + +
403D ASP* 3.3 8.8 + - - +
404D ARG* 3.1 64.1 + - - +
450D HIS* 3.8 13.1 - - - -
8404D DMS 5.3 4.7 + - - -
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Residues in contact with LEU 401 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369D GLU* 4.7 4.9 - - + +
372D MET* 3.6 33.0 - - + -
373D VAL* 4.0 18.6 - - + -
376D ILE* 3.3 20.4 - - + -
397D LEU* 3.1 39.0 + - + +
398D TRP* 3.6 5.4 - - - +
400D THR* 1.3 75.8 - - + +
402D CYS* 1.3 58.1 + - - +
404D ARG* 3.2 6.0 + - + +
405D TYR* 2.8 58.1 + - + +
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Residues in contact with CYS 402 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301D TRP* 3.9 0.5 - - - -
376D ILE* 4.6 3.6 - - - -
387D VAL* 4.3 0.4 - - - -
398D TRP* 2.8 61.7 + - - +
399D TYR* 3.8 1.8 - - - +
401D LEU* 1.3 75.8 - - - +
403D ASP* 1.3 63.6 + - - +
405D TYR* 5.2 1.1 - - - -
406D GLY* 2.9 19.2 + - - +
407D LEU* 3.2 31.4 + - + +
409D VAL* 3.6 20.4 - - + -
452D SER* 3.6 19.9 - - - +
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Residues in contact with ASP 403 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301D TRP* 2.9 26.9 + - - +
306D PRO* 3.6 4.0 - - - +
308D LEU* 3.6 12.3 - - + +
329D ASP* 4.6 10.2 - - - +
399D TYR 2.7 21.2 + - - +
400D THR* 3.4 8.2 - - - +
402D CYS* 1.3 75.0 - - - +
404D ARG* 1.3 63.0 + - + +
450D HIS* 2.7 26.9 + - - +
451D PRO* 3.3 24.9 - - + +
452D SER* 2.7 43.5 + - - -
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Residues in contact with ARG 404 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D ASP* 2.8 35.8 + - - +
306D PRO* 3.5 15.8 - - - +
308D LEU* 3.6 23.1 - - + +
310D ARG* 4.1 1.4 - - - +
329D ASP* 2.9 31.3 + - - +
400D THR* 3.1 38.3 + - - +
401D LEU* 3.2 7.5 + - + +
403D ASP* 1.3 77.3 - - + +
405D TYR* 1.3 67.5 + - + +
406D GLY 3.3 0.4 - - - -
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Residues in contact with TYR 405 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303D ALA 4.3 0.3 - - - +
306D PRO* 3.8 10.0 - - - +
373D VAL* 3.7 25.9 - - + +
376D ILE* 3.7 27.6 - - + -
377D LEU* 3.7 20.1 - - + +
380D LYS* 3.1 26.3 + - + -
401D LEU* 2.8 51.4 + - + +
402D CYS* 5.2 0.7 - - - -
404D ARG* 1.3 78.4 - - + +
406D GLY* 1.3 59.4 + - - +
707D ALA* 3.4 40.4 + - + -
708D TRP* 4.3 12.2 - + + -
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Residues in contact with GLY 406 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301D TRP* 4.2 3.6 - - - -
303D ALA* 3.6 20.8 - - - +
306D PRO* 3.8 17.3 - - - -
380D LYS* 2.9 25.5 + - - -
402D CYS 2.9 11.8 + - - -
404D ARG 3.3 1.6 - - - -
405D TYR* 1.3 76.9 - - - +
407D LEU* 1.3 65.4 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il